RetrogeneDB ID:

retro_opri_487

Retrocopy
location
Organism:Southern American pika (Ochotona princeps)
Coordinates:scaffold_13704:12041..12489(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:RPS13
Ensembl ID:ENSOPRG00000000162
Aliases:None
Description:ribosomal protein S13 [Source:HGNC Symbol;Acc:10386]


Retrocopy-Parental alignment summary:






>retro_opri_487
ATGGGTCGCATGCACGCTCCCGGGAAGGGCCTGTCCCAGTTGGCTCTACTCTATCACCACAGCATCCCCACCTGGCTGAA
GCTGATGTCTGAAGTGAAGGAGCAGATTTACAAACTGGCCAAGAAGGGCCTGACTCCCTCCCAGATCGGTGTGATCCTGA
GGGACTCCCATGGCGTCTCTCAGGTGTGTTTCGGGATAGGCAATAAGATCTTGAGGATCCTGAAGTCCAAAGGCCTGGCT
CCTGATCTTCCTGAAGCTCTGTGTCATTTAATTAAGAAAGCCGTTGCTGTGTGGAAGCACCTCGAGTGGAACAGAAAGGA
TAAGGATGCCAAATCCATCTGATTCTGATAGAGAGCCGCATTCACCAATTGGCTCGATACTACAAGACTAAGCGGGTCCT
CCCCCAAACTGGAAATATGAGCCATCCACAGCCTCTGCCCTGGTGGCA

ORF - retro_opri_487 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 85.62 %
Parental protein coverage: 100. %
Number of stop codons detected: 0
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalMGRMHAPGKGLSQSALPYRRSVPTWLKLTSDDVKEQIYKLAKKGLTPSQIGVILRDSHGVAQVRFVTGNK
MGRMHAPGKGLSQ.AL.Y..S.PTWLKL.S..VKEQIYKLAKKGLTPSQIGVILRDSHGV.QV.F..GNK
RetrocopyMGRMHAPGKGLSQLALLYHHSIPTWLKLMSE-VKEQIYKLAKKGLTPSQIGVILRDSHGVSQVCFGIGNK
ParentalILRILKSKGLAPDLPEDLYHLIKKAVAVRKHLERNRKDKDAK-FRLILIESRIHRLARYYKTKRVL-PPN
ILRILKSKGLAPDLPE.L.HLIKKAVAV.KHLE.NRKDKDAK...LILIESRIH.LARYYKTKRVL.PPN
RetrocopyILRILKSKGLAPDLPEALCHLIKKAVAVWKHLEWNRKDKDAK<IHLILIESRIHQLARYYKTKRVL<PPN
ParentalWKYESSTASALVA
WKYE.STASALVA
RetrocopyWKYEPSTASALVA

Legend:
*Stop codon
>Forward frameshift by one nucleotide
<Reverse frameshift by one nucleotide






RNA-Seq - click to see more details

Ochotona princeps was not studied using RNA-Seq expression data.

ChIP-Seq - click to see more details

Ochotona princeps was not studied using ChIP-Seq data.

EST - click to see more details

Ochotona princeps was not studied using EST data.

TSS - click to see more details

Ochotona princeps was not studied using FANTOM5 data.

Lab - click to see more details

retro_opri_487 was not experimentally validated.

Retrocopy orthology:
Ochotona princeps does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.
Parental genes homology:
Parental genes homology involve 35 parental genes, and 161 retrocopies.

Species Parental gene accession Retrocopies number
Caenorhabditis elegans C16A3.91 retrocopy
retro_cele_6,
Ailuropoda melanoleuca ENSAMEG000000028953 retrocopies
retro_amel_1451, retro_amel_1788, retro_amel_694,
Bos taurus ENSBTAG000000403085 retrocopies
retro_btau_1286, retro_btau_266, retro_btau_284, retro_btau_46, retro_btau_784,
Choloepus hoffmanni ENSCHOG000000087214 retrocopies
retro_chof_1484, retro_chof_1497, retro_chof_1644, retro_chof_2359,
Callithrix jacchus ENSCJAG000000095641 retrocopy
retro_cjac_356,
Cavia porcellus ENSCPOG000000000233 retrocopies
retro_cpor_1535, retro_cpor_400, retro_cpor_526,
Dipodomys ordii ENSDORG000000025073 retrocopies
retro_dord_397, retro_dord_57, retro_dord_759,
Equus caballus ENSECAG0000001492812 retrocopies
retro_ecab_1037, retro_ecab_1047, retro_ecab_1065, retro_ecab_1066, retro_ecab_170, retro_ecab_304, retro_ecab_696, retro_ecab_777, retro_ecab_804, retro_ecab_822, retro_ecab_891, retro_ecab_954,
Felis catus ENSFCAG000000053702 retrocopies
retro_fcat_407, retro_fcat_598,
Homo sapiens ENSG000001107006 retrocopies
retro_hsap_1499, retro_hsap_1574, retro_hsap_2098, retro_hsap_251, retro_hsap_3242, retro_hsap_388,
Gorilla gorilla ENSGGOG000000074503 retrocopies
retro_ggor_127, retro_ggor_2207, retro_ggor_303,
Latimeria chalumnae ENSLACG000000171741 retrocopy
retro_lcha_2,
Loxodonta africana ENSLAFG000000268813 retrocopies
retro_lafr_1179, retro_lafr_382, retro_lafr_511,
Macropus eugenii ENSMEUG000000149862 retrocopies
retro_meug_635, retro_meug_797,
Microcebus murinus ENSMICG000000037168 retrocopies
retro_mmur_1109, retro_mmur_1620, retro_mmur_172, retro_mmur_460, retro_mmur_588, retro_mmur_85, retro_mmur_880, retro_mmur_904,
Myotis lucifugus ENSMLUG000000097513 retrocopies
retro_mluc_174, retro_mluc_2470, retro_mluc_899,
Macaca mulatta ENSMMUG000000225472 retrocopies
retro_mmul_330, retro_mmul_40,
Monodelphis domestica ENSMODG000000070786 retrocopies
retro_mdom_1108, retro_mdom_1150, retro_mdom_1895, retro_mdom_1965, retro_mdom_566, retro_mdom_599,
Mustela putorius furoENSMPUG000000133161 retrocopy
retro_mputfur_181,
Mus musculus ENSMUSG0000009086219 retrocopies
retro_mmus_1062, retro_mmus_1124, retro_mmus_1526, retro_mmus_1563, retro_mmus_1980, retro_mmus_2210, retro_mmus_2642, retro_mmus_2830, retro_mmus_2831, retro_mmus_2832, retro_mmus_2906, retro_mmus_3050, retro_mmus_3092, retro_mmus_3153, retro_mmus_3236, retro_mmus_328, retro_mmus_3423, retro_mmus_775, retro_mmus_807,
Nomascus leucogenys ENSNLEG000000267394 retrocopies
retro_nleu_1304, retro_nleu_1693, retro_nleu_2439, retro_nleu_858,
Ornithorhynchus anatinus ENSOANG000000076871 retrocopy
retro_oana_98,
Oryctolagus cuniculus ENSOCUG000000055366 retrocopies
retro_ocun_1337, retro_ocun_1523, retro_ocun_1929, retro_ocun_673, retro_ocun_740, retro_ocun_909,
Otolemur garnettii ENSOGAG000000021287 retrocopies
retro_ogar_1567, retro_ogar_1595, retro_ogar_1818, retro_ogar_2751, retro_ogar_3441, retro_ogar_502, retro_ogar_844,
Ochotona princeps ENSOPRG00000000162 5 retrocopies
retro_opri_1107, retro_opri_239, retro_opri_390, retro_opri_487 , retro_opri_57,
Pongo abelii ENSPPYG000000034566 retrocopies
retro_pabe_1250, retro_pabe_1298, retro_pabe_2001, retro_pabe_2012, retro_pabe_2689, retro_pabe_408,
Pteropus vampyrus ENSPVAG000000128063 retrocopies
retro_pvam_1143, retro_pvam_698, retro_pvam_880,
Rattus norvegicus ENSRNOG000000205022 retrocopies
retro_rnor_190, retro_rnor_377,
Sarcophilus harrisii ENSSHAG000000040523 retrocopies
retro_shar_183, retro_shar_298, retro_shar_589,
Sus scrofa ENSSSCG000000133815 retrocopies
retro_sscr_1209, retro_sscr_264, retro_sscr_333, retro_sscr_711, retro_sscr_738,
Ictidomys tridecemlineatus ENSSTOG000000089965 retrocopies
retro_itri_1011, retro_itri_1905, retro_itri_329, retro_itri_493, retro_itri_881,
Tupaia belangeri ENSTBEG000000077177 retrocopies
retro_tbel_1777, retro_tbel_2022, retro_tbel_3850, retro_tbel_3913, retro_tbel_4204, retro_tbel_661, retro_tbel_902,
Tarsius syrichta ENSTSYG0000001311411 retrocopies
retro_tsyr_133, retro_tsyr_1352, retro_tsyr_1447, retro_tsyr_1460, retro_tsyr_1712, retro_tsyr_1900, retro_tsyr_1967, retro_tsyr_247, retro_tsyr_51, retro_tsyr_887, retro_tsyr_904,
Tursiops truncatus ENSTTRG000000163213 retrocopies
retro_ttru_1168, retro_ttru_1435, retro_ttru_737,
Vicugna pacos ENSVPAG000000014635 retrocopies
retro_vpac_117, retro_vpac_247, retro_vpac_415, retro_vpac_473, retro_vpac_525,


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